rs17010003
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_001276451.2(DRGX):c.234+1465G>T variant causes a intron change. The variant allele was found at a frequency of 0.0406 in 152,330 control chromosomes in the GnomAD database, including 170 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.041 ( 170 hom., cov: 33)
Consequence
DRGX
NM_001276451.2 intron
NM_001276451.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.75
Genes affected
DRGX (HGNC:21536): (dorsal root ganglia homeobox) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including detection of temperature stimulus; nervous system development; and sensory perception of mechanical stimulus. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0406 (6192/152330) while in subpopulation AFR AF= 0.0513 (2131/41576). AF 95% confidence interval is 0.0494. There are 170 homozygotes in gnomad4. There are 3227 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 169 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRGX | NM_001276451.2 | c.234+1465G>T | intron_variant | ENST00000374139.8 | |||
DRGX | XM_011540089.4 | c.339+293G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRGX | ENST00000374139.8 | c.234+1465G>T | intron_variant | 2 | NM_001276451.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0406 AC: 6182AN: 152212Hom.: 169 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0406 AC: 6192AN: 152330Hom.: 170 Cov.: 33 AF XY: 0.0433 AC XY: 3227AN XY: 74488
GnomAD4 genome
?
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33
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3227
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74488
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at